I'm afraid I can't think of anything directly programming or deleting related (although I accidentally shift-deleted some stuff into oblivion lately), but I remember this blow up when I was migrating a Drupal-based website from one server to another.
For those who are unfamiliar with Drupal, it keeps almost all its dynamic content in a SQL database. The server I was migrating the site to was a sort of testing installation where I tweaked and reworked quite a lot of things, so I only wanted to move the tables containing content and user data. Now those tables don't really have a primary key, so when I carelessly - sipping my coffee and conversing with a friend - launched the copying operation in SQLFront, I effectively nuked the DB. I spent like 4 hours trying to figure out what went wrong, messing with things that were in fact working just fine, raging at the Drupal devs for not having a better migration system, before it occurred to me that there is probably something oddly wrong with the DB. Restoring the DB from a backup, copying the tables again (correctly this time) and ironing out a few glitches took about 30 minutes - talk about artificial problems